Sequence
atgc intronic sequence ATGC exonic sequence...tttgcatcgtggaaatgcgaaattatttatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA
Basic information
species | Glycine max |
transcript | GLYMA04G38360.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------tttgcatcgtggaaatgcgaaattatttatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
||| | | | | ||| | | | | | |||| || || | ||||| || ||| | || | ||| | |||||||| |||||||| || ||||| | || || | ||||||||||| ||||| || || ||||| || |||||||| ||||||||||| |||||
gtaagccttctccacaaccatctcagattcaaataagttttttttttcttttggggtgcttagccaaagctagtagctttattcactatcgccaa-ttagagataagatgatatgaccatttgacatttcccaacagGCTGAGGGAAAGAAGAGAATGAAAGCAATAGGAAGGGTTGATGTTCCTCAAGAGGCATTTATGGCTGTGTTGAAACTAGAAAAGGAGGTGCTATGAAACA
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 12
------------------------------------------------------------------------tttgcatcgtggaaatgcgaaattatt------tatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
| ||| | || || | || | | ||| | | | |||| | | || || | | ||| | | | | ||||||||||||||||||||||||||| | || || | |||||||| || |||||||| |||||||| || |||| ||| ||||||||||| |||||
gtattcttagaaaaaaacgttgtttgaccccaaaaaaaagaacttagaaaataccattttgtgtataatacataagcagtatactggctttaagttttcatagaatacaagaaatgactagtagctctgttca---ccaaaatccctttgagatctgatataataatacggcgaacagGCTGAAGGAAAGAAAAGGATGAAGGCAATAGGAAGGGTTGATGTCCCTCAAGAAGCATTCATGGCCGTGTTGAGACTGGAAAAGGAGGTGCTATGAAAGT
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 21
-tttgcatcg-tggaaatgcgaaattatttatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
| | || | || ||||||| | | ||||| ||| | | | | || || | ||| | | ||| | ||| |||| | ||| ||||| || ||||| | || |||| ||||||||| || ||||||||||||||||| ||| | ||||||||| || ||| | |||
gtatatctctctataagggcgaaatcttgatttcatgattgt----atcttcagcggt-ttctgtgttccttaaaatgagtt-----tttgttttgaac-agGCGGCAGGTAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTCTCAAACTTGAACGAGAAGTATTGTGACATC
upper sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 21
tttgcatcgtggaaatgcgaaattatttata--tgcaattgttttaatcctgattcatac-cttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA----
| | | |||| |||||| | | || | || | | | | ||| || ||| | || || | || || |||||||||||||||||||| |||||| | ||||||||||||||||| || ||||| ||||||||||| || ||||||||||||||||||||| |||||
---gtaatgaattaatgtatgtttattttttattaaaagaaaaatgatgagaaatgaaattctttccctgtgcatgactgttttctgatcatcttcttctcagGCTGAAGGAAAGAAAAGAATGAAGGCAATTGGTAAAGTTGATGTACCTCAAGAGGCTTTCATGGCTGTCTTGAAACTTGAAAAGGAGGTATTATGATTGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|193581298|gb|FK537863.1|FK537863EST: GTGGGGATATTTCGAGAAAAAAGAAATTGCTTAAGAAACAG GCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAA
genomic: GTGGGGATATTTCGAGAAAAAAGAAATTGCTTAAGAAACAGgtatgatcag ... ctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA
tctgtctcc CT-rich tract
tcataatagtattat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcatcgtggaaatgcgaaattatttatatgcaattgttttaatcctgattcataccttagattgctcataatagtattatcgtctgtctccaaccagGCTGAAGGAAAGAAAAGGATGAAGTCTATTGGTAAAGTTGATGTTCCCCAAGAAGCTTTCATGGCAGTTTTGAAACTTGAAAAGGAGGTAATATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
tttgcat
- - - - - -gaaatgc
- - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - - cctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -catacct